The X Factor
by Lady Jaye1
Summary: AU GI Joe x XMen Alternate universes collide when the Joe's world meets the XMen. The Joes soon discover a complicated world where some of the people they know are even mutants...
1. Prologue

_Disclaimer: I don't own GI Joe or any of the Marvel Universe._

_GI Joe/X-Men: AU crossover. Alternate universes collide when a breach opens up between the Joes' world, and the world of the X-Men. They soon discover a complicated world where mutants exist and the people they thought they knew are either mutants...or not._

**The X-Factor**

**Chapter 1:** Prologue

_Location:_ Tokyo, Japan  
_When:_ Six days ago, 22:38

The man slowly drank his cup of sake as his eyes darted watchfully around the room. He wasn't too concerned; he could handle most trouble that came his way. Unfortunately, trouble always seemed to have had a rude preference for him. That was all right though. He thrived on the adrenaline.

He smelled the newcomer just as he walked into the bar. His white ninja garments glowed eerily in the darkened, smoke filled bar, his two sheathed katana clearly visible to the observer.

The man smirked briefly as he stuck a Cuban cigar in his mouth and lit it. He had to hand it to Nick Fury, the man sure knew how to pick a good cigar.

"Smoking again Logan-san?"

Logan, also known as Wolverine, smirked in reply as he pushed a chair towards the newcomer. He had been expecting this man.

"Have a drink Arashikage-san, it's on the house. I happen to know the bar owner." Which in fact, was part of the reason that Thomas Arashikage was even here in the first place. The bar itself was located in a less than reputable section of Tokyo. The people here didn't ask questions.

Tommy hesitated a brief second before pulling his white face mask off. There were very few places where he could walk around publicly. Unlike Logan, his mutant characteristics were clearly visible.

"What has your ex-wife been up to now?" Tommy asked dryly. Logan grimaced as he pushed a bottle of sake towards the green skinned ninja.

"The usual. Viper's got her hands in every black market activity in Japan. The problem is, she's been secretly funding a new group of the Brotherhood." A pair of golden eyes regarded Logan seriously as he took a sip of sake.

"The Arashikage Clan has some spies within her network," Tommy admitted. "But you already knew that."

"What can you tell me?"

"This new group calls themselves The Hand of God. Their leader calls herself the Baroness."

"Great. Fanatics. That's just what we need. Viper's not the type to get involved in any kind of ideological battle. She must be making a hell of a profit," Logan growled.

"It gets better. Our old friend Magneto has also been funneling money to them. And...I don't know if it's related Logan-san, but I think something else is going on," Tommy added. "I think Sinister is up to something, but I don't know what. We've heard his name mentioned among several high ranking members of the Brotherhood." Logan swore under his breath. Xavier wasn't going to be happy about this one.

The two men traded some more information before sitting quietly, each in their own thoughts. The ninja had himself been a brief member of the Brotherhood before Charles Xavier had found him. Now he had associated himself with the X-Men, but still spent most of his time in Japan. After a while, Tommy decided to ask the question that was on nearly every mutant's mind.

"Have they…had any luck finding a cure for the Legacy virus?" he asked. Logan shook his head.

"Hank and Edwin have been working non stop. They say that they're getting closer, but we'll see." There was a pause.

"Logan-san," Tommy said quietly, "Cobra's opened up a new branch in Machida." Logan growled again. Cobra was an anti-mutant terrorist group that had originated in the United States and spread to Europe, Asia, and pockets of South America and Australia. The US and the EU governments had done little against the organization because too many people shared their anti-mutant views.

After a few more drinks, the Arashikage ninja finally stood up and bowed to the older man.

"Thank you for the sake, Logan-san. Please send my regards Xavier-sensei and the others."

"Sayonara," Logan replied formally. The Canadian watched as the raven haired ninja pulled his mask back over his head and walked through the closed door. Like Kitty Pryde, Thomas Arashikage had the ability to phase through solid objects.

Quite a useful skill for a ninja.

…………………………………………………………………………………………….

_Location:_ New Orleans, Louisiana  
_When:_ Five days ago, 03:00

"LeBeau, this is the _last _time I'm saving your neck!"

"Dat's what you said last time, Sneeden."

"Well I mean it _this_ time LeBeau."

Wayne Sneeden had to hold himself back from throttling the insane Cajun mutant. Remy LeBeau merely grinned cheerfully as he thumbed through a stack of playing cards. The two men were now wandering through the near empty streets of the French Quarter.

"Gambit, my idea of a good time is _not _to save your neck from rogue members of the Thieves Guild, to get nearly drowned in Lake Pontchartrain, and to get into a fight with three Sentinels and a deranged Morlock."

"Ah, but dey certainly were d'loveliest rogue thieves dat we could ask for!" Gambit grinned. "I tink dat de blonde one liked you. Besides," he added craftily. "You weren't unconscious long enough t'drown."

Wayne rolled his eyes. At least the streets were almost empty now. LeBeau could pass as a normal human, with the definition of human being some what relative in the Cajun's case, but he himself could not. Everything about Wayne Sneeden screamed mutant, everything from his silvery white hair and pale albino skin to his bright silver eyes and pointed ears.

The neighborhood children in Alabama had delighted in tormenting him while growing up, at least until his powers had developed. They had stopped laughing then.

"LeBeau," Wayne finally warned. "What do you think would happen if I froze your tongue off?" The air crackled and froze around his outstretched fingertips.

"Den I would throw a card up yer rear end," Gambit smirked in reply.

"Oh yeah?" Wayne drawled calmly. "Then I'd tell Rogue about how you were ogling 'dem lovely rogue thieves'."

"No! Ah, I mean, I tink I'll shut up now."

The two men wandered then quietly through the streets of New Orleans. Wayne scowled darkly as they passed an old wall covered with anti-mutant graffiti. _Bigoted maggots. _After a pause, he walked over and placed a hand on the wall. Remy watched as a cold frost covered the writing, causing the paint to crumble and disintegrate from the freezing temperatures.

"Of course you realize dat someone's going t'notice tomorrow," Remy stated. Wayne shrugged as they continued down the street.

"Hell," Wayne drawled angrily, "They're damn lucky I didn't demolish the wall."

Once upon a time, Wayne Sneeden might have in the army, perhaps even a Ranger. His mutant abilities had kept him from that. The recruiter had laughed at him when he'd shown up in the office to enlist at age seventeen. He had eventually been discovered by Professor Charles Xavier and now served as a proud member of the X-Men. Taking the code name of Beach Head, he commanded one of the X-Men's three strike teams, with Storm and Cyclops commanding the other two. He had also served as a brief member of X-Force and had worked with several people from SHIELD, including Nick Fury.

Sitting around with Fury and Logan in a smoke filled room was always one of his highlights. Wayne loved nothing more than to share a beer with the two older men while they smoked and shared war stories. He had quite a few to tell himself, but it was always more interesting to listen to the other two talk. Occasionally Sean Cassidy, also known as Banshee, would join them. The Irishman had many stories of his own from the time he had worked for Interpol during the Cold War.

"We need to find Sarai," Wayne said suddenly. "I told her to stay out of trouble, but you know how the kid is." Remy flipped through his cards once more before pocketing them. He was a little worried about the girl too. He, Wayne, Ororo Munroe and Kurt Wagner had come across the girl when they were in Jerusalem a few years ago. She had been eight years old then and had been abandoned by her aunt and uncle because of her mutant appearance.

She had tried to pick Wayne's pocket, which as she had found, was a grave mistake. Still, the four X-Men had taken her back to New York where she surprisingly adopted the grumpy Alabaman as a father figure. Wayne had soon found himself unexpectantly in the role of a parent. It was perhaps the most daunting challenge he had ever undertaken.

Now the feline girl was eleven and still a pain in the ass.

"If you hadn't been teaching her any of your tricks Remy, I wouldn't be having half the problems I do."

"Calm down Beach, it's not m'fault dat she's a natural thief. She could go far in de Thieves Guild."

"I'd kill her first."

The two mutants eventually found the girl, or rather, she found them. She pounced out from the shadows and attempted to tackle Wayne. He briefly considered gluing her feet to the ground in a sheet of ice, but instead chose to wrap a strong arm around her head.

"Where have you been?" he commanded, trying to hide his concern.

"Staying out of trouble," she answered innocently. Her feline ears perked up nonchalantly as her golden eyes danced mischievingly at him. Wayne hid a smirk as he examined her.

"Did you steal anything?" he asked sternly.

"Never!"

Wayne raised an eyebrow and her ears wilted slightly. Her clawed hands reached into her purple jacket reluctantly and pulled out a necklace.

"I took it from the mean blonde haired lady that was trying to kill you and Remy," she explained meekly. Gambit began to laugh heartily, causing Wayne to glare at him. It didn't last long as his glare turned into another smirk.

"You stole that from a member of the Thieves Guild?" he drawled. The girl smirked back up at him as she held up the necklace.

"Yeah, can I keep it?" she asked. Wayne debated on his response. Stealing was wrong, but then again...she _had _stolen it from a thief, who had most likely stolen it from someone else, perhaps even another thief.

"I suppose you can keep it," he finally assented. There was really no way they would be able to track down the real owner. "But just this once," he warned. "I'm only letting you do this because she was a thief and tried to kill us."

"I'm a thief and I've tried t'kill you," Remy pointed out.

"You're a thief and your unintentional murderous techniques failed because you were distracted by a short skirt with long legs." Remy had once sabotaged the Danger Room when Wayne had been working out. The thief's practical joke hadn't gone as planned because Rogue had decided to interfere with his scheme. Beach Head had ended up chasing the crazy Cajun thief around the Mansion until an unamused Storm finally put a stop to it.

Sarai grinned triumphantly as she placed the jewelry around her neck. Then she yawned and tugged on Wayne's jacket.

"Can we go home now?" she asked. "Jean and Scott are going to take our class on a field trip on Monday." Wayne scowled slightly at the mention of Cyclops. Like Logan, he didn't get along too well with the man. He respected Jean Grey, although he didn't have Logan's same feelings for her, but he couldn't understand what she saw in that arrogant prissy boyscout that went by the name of Scott Summers.

"We'll be back in time for that," Wayne said instead. "Where are they taking you?"

"The zoo."

"Make sure you leave Summers there."

"With the monkeys?" she asked innocently.

"No, he deserves his own special exhibit."

"So do you," Remy pointed out.

"Shut up LeBeau."

"Wayne," the girl asked. "Can you make it snow? _Please?_" Wayne looked down at the expectant child before smirking at her. His bright eyes clouded over momentarily as they made their way down the street. Seconds later, a light snowfall was blanketing the city of New Orleans, much to the delighted eyes of the eleven year old child.

……………………………………………………………………………………………………

_Where:_ Our universe, An undisclosed location  
_When:_ Four days ago, 10:21

Destro paused outside of the chamber, wondering what madness Cobra Commander was up to now. The man had been in close contact with Dr. Mindbender the last three days. Yesterday, there had been an undocumented visitor in to see the snake. The Scotsman briefly eyed the two guards at the door before walking in unannounced. The audacity of the man, what was he up to now?

Alexander had seen the visitor, which he had described as "not human". Destro had decided to investigate this himself.

"Cobra Commander..." he started. He was interrupted by a smooth and charismatic voice that he distrusted immediately. The voice held an undertone of corrupt madness.

"Destro, Destro...I'm so glad you came."

"I'm sorry to say that I don't share your enthusiasm, Cobra Commander," Destro replied dryly. He paused in front of the tall dais where the object of his hatred sat garbed in a blue mask. Zartan and Zarana stood at his side as a vigilant Storm Shadow kept watch.

"Please Destro, don't ruin my good cheer. I have such good news to tell you."

"Good news?" Destro asked, with just a slight undertone of sarcastic disbelief.

Cobra Commander motioned with his hand and a figure stepped forth from the shadows. _I see, _Destro thought. _So this is the man that Alexander was talking about. _He used the word 'man' loosely. The tall creature seemed to have a body of pure rock and a gargantuan head to match.

"His real name is Lucio Donati, but he is most often referred to as 'il doge'." Il doge...the dog. "He's a mutant that has come to me with an offer from his...employer."

"Mutant?" Destro asked suspiciously. Had Mindbender been experimenting again?

"It's quite natural, I assure you," Cobra Commander continued. "In his universe, many people are being born as mutants. They are the next evolution of humankind...Homo Superior to be exact. His employer, quite accidentally really, created a bit of a tunnel between our universe and his."

"And this employer, who is he?" Destro asked.

"He calls himself Mr. Sinister, but we have yet to meet," Cobra Commander continued. "We are pursuing a...diplomatic relationship, if you will. Have a seat Destro, no in fact, I'm calling a meeting. There is much for all of us to discuss."

Destro studied the other man beneath his steel mask. What madness was in the works? Whatever it was, he was sure that he didn't want to be involved.

………………………………………………………………………………………………

_Where:_ Our universe, The GI Joe PIT  
_When: _Three days ago, 09:46

"Ah, come on Lifeline, have some mercy here."

"I'm sorry Rock 'N' Roll, but you're going to have to stay off that leg for at least a week."

"No rest for the wicked, eh?" another voice asked.

"Shut up Dusty."

"You two know my rules," Dr. Edwin Steen said patiently. "No fighting in the infirmary."

"Well he started it," Rock 'N' Roll complained.

"I did not," Dusty shot back. Lifeline sighed. Even he felt the urge to whack the two soldiers over their heads.

"What are you two, children?" he asked. The two men grinned at him. Edwin supposed it could have been worse. He could have had Gung Ho and Beach Head in the infirmary. _That _would have been a disaster waiting to happen.

"Well anyway," Lifeline said, "You two had better get cleaned up. Hawk's going to have a small meeting in an hour. Snake Eyes, Jinx, and Kamakura have some new information that they're going to share with us."

"Some new Intel, huh?" Dusty asked. "I guess it's about time. Cobra's been too quiet the last month."

"I'm ready to kick some snake ass," Rock 'N' Roll said. "Stalker and I have a bet that I intend to win."

"What bet is that?" Dusty asked.

"Nothing much, just to see who can kill the most snakes." The two soldiers ignored the stern look of disapproval on the doctor's face. His pacifism was already well known to them. Lifeline watched them as they exited the room, with Rock 'N' Roll hopping along on a pair of crutches.

He knew the importance of stopping Cobra, of protecting the innocent from the various rogue groups running around the globe. But even so, he still didn't have to like the violence. That was why he had chosen the role of a non-combatant. He refused to use hands that killed. He was a doctor. It was his duty to save lives.

Lifeline cleaned up his area and nodded to the nurses before he left. He wondered what new information they would learn in the meeting. Knowing Cobra, he already knew he wouldn't like it.


	2. The Countdown Begins

_Disclaimer: I don't own GI Joe or any of the Marvel Universe._

**The X-Factor**

**Chapter 2:** The Countdown begins

_Where:_ Our universe, The GI Joe PIT  
_When: _Three days ago, 11:00

"So what exactly took place in this secret meeting of Cobra's?" Lady Jaye asked. Duke and Hawk exchanged glances before the former nodded slightly at Snake Eyes. The ninja silently placed a packet of photos on the table.

"What you see there," Duke said matter of factly, "Are Cobra's new associates." The other Joes peered at the photographs as they were passed around. They showed Cobra Commander walking with two strange figures. One was a tall, pale man with long raven hair and glowing red eyes. The other…

"Has Mindbender been experimenting again?" Stalker asked. Duke's lips pursed into a thin line before answering.

"We don't know," he admitted reluctantly. "What evidence we have appears to suggest that the man and the…creature…with Cobra Commander are not in fact a result of Mindbender's genetic experiments. However…"

Lifeline listened with half an ear as he studied the photographs. The 'creature,' as Duke had called it, was huge. It easily towered over Cobra Commander and Destro. Its skin appeared to be hard granite and its eyes, pitch black, were embedded deep into the craggy face.

"He's an ugly one," Dusty muttered. Beach Head gave a snort as he crossed his arms and stared hard at the two men at the head of the round table.

"How could they be anything besides one of Mindbender's experiments?" the Ranger drawled. "If you expect me to believe that this is some kind of hocus pocus crap…"

"He just said that he doesn't know Beach Head," Flint said sharply. The balaclava hid a wry smirk as the Ranger replied back.

"Then we should find out then, shouldn't we?" Wayne Sneeden said dryly. This received a set of glares, none of which fazed the Ranger in the slightest.

"Beach Head's right," Cover Girl finally said. "We can't jump to conclusions yet."

"Do we know anything else yet Duke?" Scarlett asked. The blonde in question tapped a key on his laptop and brought up several images on the large flat screen behind him.

"These photos were taken in the Xizang Autonomous region on the Chinese-Indian border," he said. "Cobra's using the Himalayas as cover." With another tap of his finger, Duke brought up a series of aerial maps as well as a partial blueprint of the base.

"Most of the compound is tunneled into the mountains," Hawk continued for Duke. "Kamakura and Jinx are still there, trying to find out more."

"Are we sending in a team?" Flint asked.

"Once we have more information," Hawk said. "Then yes."

……………………………………………………………………………………………

_Where:_ The X-Men universe, The Xavier Institute for Higher Learning  
_When: _Three days ago, 14:36

"Are Wayne and Scott still arguing?" Dr. Edwin Steen asked. His blue companion chuckled as he moved a piece on the chess board between them.

"I believe Logan has joined it now," Dr. Henry "Hank" McCoy answered. "Knowing our short Canadian friend, he undoubtedly has taken Wayne's side."

"When did Logan get back?" Lifeline asked. He moved one of his pawns.

"It was early this morning." The Beast studied the board for a moment before continuing. "He was in Japan again."

Edwin winced as Hank captured one of his knights. Beast briefly studied the other mutant, who, unlike him, showed no physical sign of his mutation.

"I was under the impression that you had a class to teach today," Hank said. Edwin studied the board for a split second before swiping one of Hank's rooks.

"Excellent choice, my friend," Hank McCoy said. "At least, it would have been…" He moved a knight closer to Edwin's queen. Lifeline hid a smirk as he hoped the other doctor would fall into his trap.

The two doctors were fairly evenly matched. Hank had the higher intelligence but Edwin had the faster brain.

"Are you still having nightmares?" Hank finally asked quietly. Edwin's fingers hesitated a moment above his bishop, then picked it up and moved it.

"I'll take that as a yes," the Beast said. He intertwined his enormous blue fingers as he studied Lifeline with the same intensity that he had formerly been giving to the chess game. Edwin sighed.

"The Professor has scanned me more than once, as has Jean," he stated, "But…"

"But they haven't found anything," Hank finished.

"…No."

"It wasn't your fault Edwin."

"Those are cheap words Hank."

"It was Apocalypse, not you."

"It was still _my_ body, how the hell wasn't it me?" Edwin asked sharply. Beast opened his mouth to say something further, but decided against it. The two men played silently for a few minutes before Hank decided to change the subject.

"This is quite surprising," Hank McCoy observed as he prepared to move another knight. "We have managed to play for nearly twenty minutes without any interruptions…"

_Bamf._

"Ich heisse Errol Flynn!" Kurt Wagner shouted. 'Errol Flynn' sailed over the two doctors' heads as he brandished a fencing epee, his tail flowing behind him. The blue mutant known as Nightcrawler gave the sword a few flicks at his imaginary opponent before teleporting away, leaving behind his signature scent of brimstone.

Hank's furry fingers were still paused above the spot where he was intending to place his knight.

"You spoke too soon," Edwin informed him dryly. Hank set down his chess piece as shouts of random German floated into the room from elsewhere in the mansion, followed by what suspiciously sounded like Rogue and Gambit yelling dire threats to the rampaging German mutant. Suddenly, there was a crash, followed by a muffled cry of 'Mein Gott!'

Then there was silence.

Seconds later, a female head poke up out of the chess board, causing both men to jump.

"Kitty!" Edwin exclaimed. "I wish you wouldn't do that!" Kitty Pryde flashed an innocent smile as she phased the rest of the way out of the floor and sat in a nearby chair.

"A little blue bird told me you two were in here," she said.

"Pray, did it carry a sword and speak German?" Hank asked dryly.

"How did you know?" Kitty asked in mock surprise.

"An educated guess."

"We noticed that it suddenly became mysteriously quiet after your little bird shouted 'Mein Gott'," Edwin said. Kitty's smile widened as her eyes gave a mischievous twinkle.

"That would be when I accidentally phased through Kurt while he and Remy were having a duel," she answered.

"Accidentally?" Hank questioned. Edwin sighed.

"Lighten up Ed," Kitty grinned. "They're just having fun. They're not _intentionally_ trying to kill each other."

"Even so…" Lifeline started.

"You're foot's tapping," Shadowcat suddenly pointed out. "So's your finger."

"Yes," Hank added thoughtfully. "I'm surprised that he's sat still this long." Edwin Steen ignored the commentary as he vainly tried to protect his queen from his furry blue companion. Just because his mutant power happened to be superspeed didn't mean he couldn't sit still…

Edwin watched with growing impatience as Hank's hand appeared to move with agonizing slowness.

"Checkmate," Beast said.

And none too soon. Edwin's other foot was starting to fidget as well.

"I suppose we should return to the lab," Hank said regretfully. The two doctors were currently working on a cure for the Legacy virus that was running through the mutant population.

"_X-Men, please report to the boardroom."_

The three mutants looked at each other as the voice of Charles Xavier entered their minds.

"Never a dull moment when you're an X-Man," Shadowcat remarked. As Lifeline grabbed a hold of each of his friends and whisked them down the corridor, he couldn't help but agree.

…………………………………………………………………………………………..

_Where:_ Our universe, the Xizang Autonomous Region, China  
_When: _Three days ago, 21:08

The man formerly known as Nathaniel Essex sipped on his tea as the blue garbed mad man next to him continued to prattle on about their future "relationship." However, as much as Cobra Commander might choose to believe, Mr. Sinister was anything but a pawn.

Sinister could sense the distrust emanating from the Scotsman to his right. Destro had said little to the mutant yet, to which he was actually grateful. Cobra Commander was a tool to be used and tossed away, nothing more.

However, if Destro proved trustworthy, he could make a useful servant.

Mr. Sinister hid a smile as he pondered on what to do with this world. With Apocalypse's defeat over a year ago, as well as being presumed dead, he was free to experiment as he wished.

He hadn't expected to open up a gateway to another universe.

Nor had he expected it to be a world devoid of mutants.

Mr. Sinister, an immortal mutant, was well known for his genetic 'experiments', particularly if it involved the Summers' bloodline. This new Earth, free of the mutant gene, was his to play with. To experiment with.

The possibilities were endless.

……………………….

_**Notes:**_

"_Ich heisse Errol Flynn!" (My name is Errol Flynn!)_

"_Mein Gott!" (My God!)_


End file.
